OpenRaiser/Intern-Atlas huggingface dataset:
Reconstruction and Analysis of Cancer-specific Gene Regulatory Networks from Gene Expression Profiles
Venue: arXiv cs.SY 2013
Year: 2013

The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput data generated by microarray experiments fueled researchers to use whole-genome gene expression profiles to understand cancer and to reconstruct key cancer-specific gene regulatory network. Now, the researchers are taking a keen interest in the development of algorithm for the reconstruction of gene regulatory network from whole genome expression profiles. In this study, a cancer-specific gene regulatory network (prostate cancer) has been constructed using a simple and novel statistics based approach. First, significant genes differentially expressing them self in the disease condition has been identified using a two-stage filtering approach t-test and fold-change measure. Next, regulatory relationships between the identified genes has been computed using Pearson correlation coefficient. The obtained results has been validated with the available databases and literature. We obtained a cancer-specific regulatory network of 29 genes with a total of 55 regulatory relations in which some of the genes has been identified as hub genes that can act as drug target for the cancer diagnosis.
Flooding edge or node weighted graphs
Venue: arXiv cs.CV 2013
Year: 2013

Reconstruction closings have all properties of a physical flooding of a topographic surface. They are precious for simplifying gradient images or, filling unwanted catchment basins, on which a subsequent watershed transform extracts the targeted objects. Flooding a topographic surface may be modeled as flooding a node weighted graph (TG), with unweighted edges, the node weights representing the ground level. The progression of a flooding may also be modeled on the region adjacency graph (RAG) of a topographic surface. On a RAG each node represents a catchment basin and edges connect neighboring nodes. The edges are weighted by the altitude of the pass point between both adjacent regions. The graph is flooded from sources placed at the marker positions and each node is assigned to the source by which it has been flooded. The level of the flood is represented on the nodes on each type of graphs. The same flooding may thus be modeled on a TG or on a RAG. We characterize all valid floodings on both types of graphs, as they should verify the laws of hydrostatics. We then show that each flooding of a node weighted graph also is a flooding of an edge weighted graph with appropriate edge weights. The highest flooding under a ceiling function may be interpreted as the shortest distance to the root for the ultrametric flooding distance in an augmented graph. The ultrametric distance between two nodes is the minimal altitude of a flooding for which both nodes are flooded. This remark permits to flood edge or node weighted graphs by using shortest path algorithms. It appears that the collection of all lakes of a RAG has the structure of a dendrogram, on which the highest flooding under a ceiling function may be rapidly found.
Reduce Meaningless Words for Joint Chinese Word Segmentation and Part-of-speech Tagging
Venue: arXiv cs.CL 2013
Year: 2013

Conventional statistics-based methods for joint Chinese word segmentation and part-of-speech tagging (S&T) have generalization ability to recognize new words that do not appear in the training data. An undesirable side effect is that a number of meaningless words will be incorrectly created. We propose an effective and efficient framework for S&T that introduces features to significantly reduce meaningless words generation. A general lexicon, Wikepedia and a large-scale raw corpus of 200 billion characters are used to generate word-based features for the wordhood. The word-lattice based framework consists of a character-based model and a word-based model in order to employ our word-based features. Experiments on Penn Chinese treebank 5 show that this method has a 62.9% reduction of meaningless word generation in comparison with the baseline. As a result, the F1 measure for segmentation is increased to 0.984.
Exploiting Self-Interference Suppression for Improved Spectrum Awareness/Efficiency in Cognitive Radio Systems
Venue: arXiv cs.NI 2013
Year: 2013

Inspired by recent developments in full-duplex communications, we propose and study new modes of operation for cognitive radios with the goal of achieving improved primary user (PU) detection and/or secondary user (SU) throughput. Specifically, we consider an opportunistic PU/SU setting in which the SU is equipped with partial/complete self-interference suppression (SIS), enabling it to transmit and receive/sense at the same time. Following a brief sensing period, the SU can operate in either simultaneous transmit-and-sense (TS) mode or simultaneous transmit-and-receive (TR) mode. We analytically study the performance metrics for the two modes, namely the detection and false-alarm probabilities, the PU outage probability, and the SU throughput. From this analysis, we evaluate the sensing-throughput tradeoff for both modes. Our objective is to find the optimal sensing and transmission durations for the SU that maximize its throughput subject to a given outage probability. We also explore the spectrum awareness/efficiency tradeoff that arises from the two modes by determining an efficient adaptive strategy for the SU link. This strategy has a threshold structure, which depends on the PU traffic load. Our study considers both perfect and imperfect sensing as well as perfect/imperfect SIS.
Cognitive Beamforming for Multiple Secondary Data Streams With Individual SNR Constraints
Venue: arXiv cs.IT 2013
Year: 2013

In this paper, we consider cognitive beamforming for multiple secondary data streams subject to individual signal-to-noise ratio (SNR) requirements for each secondary data stream. In such a cognitive radio system, the secondary user is permitted to use the spectrum allocated to the primary user as long as the caused interference at the primary receiver is tolerable. With both secondary SNR constraint and primary interference power constraint, we aim to minimize the secondary transmit power consumption. By exploiting the individual SNR requirements, we formulate this cognitive beamforming problem as an optimization problem on the Stiefel manifold. Both zero forcing beamforming (ZFB) and nonzero forcing beamforming (NFB) are considered. For the ZFB case, we derive a closed form beamforming solution. For the NFB case, we prove that the strong duality holds for the nonconvex primal problem and thus the optimal solution can be easily obtained by solving the dual problem. Finally, numerical results are presented to illustrate the performance of the proposed cognitive beamforming solutions.
The Formalization of Syntax-Based Mathematical Algorithms Using Quotation and Evaluation
Venue: arXiv cs.LO 2013
Year: 2013

Algorithms like those for differentiating functional expressions manipulate the syntactic structure of mathematical expressions in a mathematically meaningful way. A formalization of such an algorithm should include a specification of its computational behavior, a specification of its mathematical meaning, and a mechanism for applying the algorithm to actual expressions. Achieving these goals requires the ability to integrate reasoning about the syntax of the expressions with reasoning about what the expressions mean. A syntax framework is a mathematical structure that is an abstract model for a syntax reasoning system. It contains a mapping of expressions to syntactic values that represent the syntactic structures of the expressions; a language for reasoning about syntactic values; a quotation mechanism to refer to the syntactic value of an expression; and an evaluation mechanism to refer to the value of the expression represented by a syntactic value. We present and compare two approaches, based on instances of a syntax framework, to formalize a syntax-based mathematical algorithm in a formal theory T. In the first approach the syntactic values for the expressions manipulated by the algorithm are members of an inductive type in T, but quotation and evaluation are functions defined in the metatheory of T. In the second approach every expression in T is represented by a syntactic value, and quotation and evaluation are operators in T itself.
On a New Notion of Partial Refinement
Venue: arXiv cs.LO 2013
Year: 2013

Formal specification techniques allow expressing idealized specifications, which abstract from restrictions that may arise in implementations. However, partial implementations are universal in software development due to practical limitations. Our goal is to contribute to a method of program refinement that allows for partial implementations. For programs with a normal and an exceptional exit, we propose a new notion of partial refinement which allows an implementation to terminate exceptionally if the desired results cannot be achieved, provided the initial state is maintained. Partial refinement leads to a systematic method of developing programs with exception handling.
Improved Branch-and-Bound for Low Autocorrelation Binary Sequences
Venue: arXiv cs.AI 2013
Year: 2013

The Low Autocorrelation Binary Sequence problem has applications in telecommunications, is of theoretical interest to physicists, and has inspired many optimisation researchers. Metaheuristics for the problem have progressed greatly in recent years but complete search has not progressed since a branch-and-bound method of 1996. In this paper we find four ways of improving branch-and-bound, leading to a tighter relaxation, faster convergence to optimality, and better empirical scalability.
Resource Efficient LDPC Decoders for Multimedia Communication
Venue: arXiv cs.IT 2013
Year: 2013

Achieving high image quality is an important aspect in an increasing number of wireless multimedia applications. These applications require resource efficient error correction hardware to detect and correct errors introduced by the communication channel. This paper presents an innovative flexible architecture for error correction using Low-Density Parity-Check (LDPC) codes. The proposed partially-parallel decoder architecture utilizes a novel code construction technique based on multi-level Hierarchical Quasi-Cyclic (HQC) matrix with innovative layering of random sub-matrices. Simulation of a high-level MATLAB model shows that the proposed HQC matrices have bit error rate (BER) performance close to that of unstructured random matrices. The proposed decoder has been implemented on FPGA. It is very resource efficient and provides very high throughput compared to other decoders reported to date. Performance evaluation of the decoder has been carried out by transmitting JPEG images over an AWGN channel and comparing the quality of the reconstructed images with those from other decoders.
Integration of Wireless Sensor Networks with Virtual Instrumentation in a Residential Environment
Venue: arXiv cs.NI 2013
Year: 2013

This paper presents an approach to integrate wireless sensor networks (WSN) with the LabVIEW graphical development environment through a dedicated software driver. As personal constribution, a system architecture and concept implementation are described, in the context of a smart house monitoring scenario. Data acquisition is performed via the deployed wireless sensor network with focus on three main parameters: temperature, humidity and light. The data logging, monitoring and control functions are realized through a virtual instrumentation project. This also enables an easy-to-use user interface and the accesibility of data through standards-based web server technologies. The potential of remote monitoring and control through mobile terminals is opened up.
A Stochastic Geometry Framework for Analyzing Pairwise-Cooperative Cellular Networks
Venue: arXiv cs.IT 2013
Year: 2013

Cooperation in cellular networks has been recently suggested as a promising scheme to improve system performance, especially for cell-edge users. In this work, we use stochastic geometry to analyze cooperation models where the positions of Base Stations (BSs) follow a Poisson point process distribution and where Voronoi cells define the planar areas associated with them. For the service of each user, either one or two BSs are involved. If two, these cooperate by exchange of user data and channel related information with conferencing over some backhaul link. Our framework generally allows variable levels of channel information at the transmitters. In this paper we investigate the case of limited channel state information for cooperation (channel phase, second neighbour interference), but not the fully adaptive case which would require considerable feedback. The total per-user transmission power is further split between the two transmitters and a common message is encoded. The decision for a user to choose service with or without cooperation is directed by a family of geometric policies depending on its relative position to its two closest base stations. An exact expression of the network coverage probability is derived. Numerical evaluation allows one to analyze significant coverage benefits compared to the non-cooperative case. As a conclusion, cooperation schemes can improve system performance without exploitation of extra network resources.
Using Blogs to Promote Writing Skill in ESL Classroom
Venue: arXiv cs.CY 2013
Year: 2013

This study provides details on the motivational factors for using blogs as an essential tool to promote students writing skills in ESL classrooms. The study aims to discuss how using blogs may be integrated into classroom activities to promote students writing skills as well as polishing their skills. It would also illustrate the features offered in blogs as well as the motivational essence that is attached to the blogs. To achieve the aim of the study, a semi-structured interview protocol was used to collect the required qualitative data. The findings of the study would serve as an insistent reminder that the blogs which have been clearly underlined in the curriculum should be re-orchestrated more effectively again by the teachers of English as a Second Language (ESL).
Near-Optimal Truthful Auction Mechanisms in Secondary Spectrum Markets
Venue: arXiv cs.NI 2013
Year: 2013

In this work, we study spectrum auction problem where each request from secondary users has spatial, temporal, and spectral features. With the requests of secondary users and the reserve price of the primary user, our goal is to design truthful mechanisms that will either maximize the social efficiency or maximize the revenue of the primary user. As the optimal conflict-free spectrum allocation problem is NP-hard, in this work, we design near optimal spectrum allocation mechanisms separately based on the following techniques: derandomized allocation from integer programming formulation, its linear programming (LP) relaxation, and the dual of the LP. We theoretically prove that 1) our near optimal allocation methods are bid monotone, which implys truthful auction mechanisms; and 2) our near optimal allocation methods can achieve a social efficiency or a revenue that is at least $1-\frac{1}{e}$ times of the optimal respectively. At last, we conduct extensive simulations to study the performances (social efficiency, revenue) of the proposed methods, and the simulation results corroborate our theoretical analysis.
Enhanced Predictive Ratio Control of Interacting Systems
Venue: arXiv cs.SY 2013
Year: 2013

Ratio control for two interacting processes is proposed with a PID feedforward design based on model predictive control (MPC) scheme. At each sampling instant, the MPC control action minimizes a state-dependent performance index associated with a PID-type state vector, thus yielding a PID-type control structure. Compared to the standard MPC formulations with separated single-variable control, such a control action allows one to take into account the non-uniformity of the two process outputs. After reformulating the MPC control law as a PID control law, we provide conditions for prediction horizon and weighting matrices so that the closed-loop control is asymptotically stable, and show the effectiveness of the approach with simulation and experiment results.
Data Leak Aware Crowdsourcing in Social Network
Venue: arXiv cs.SI 2013
Year: 2013

Harnessing human computation for solving complex problems call spawns the issue of finding the unknown competitive group of solvers. In this paper, we propose an approach called Friendlysourcing to build up teams from social network answering a business call, all the while avoiding partial solution disclosure to competitive groups. The contributions of this paper include (i) a clustering based approach for discovering collaborative and competitive team in social network (ii) a Markov-chain based algorithm for discovering implicit interactions in the social network.
Normalized Online Learning
Venue: arXiv cs.LG 2013
Year: 2013

We introduce online learning algorithms which are independent of feature scales, proving regret bounds dependent on the ratio of scales existent in the data rather than the absolute scale. This has several useful effects: there is no need to pre-normalize data, the test-time and test-space complexity are reduced, and the algorithms are more robust.
Domino Tatami Covering is NP-complete
Venue: arXiv cs.CC 2013
Year: 2013

A covering with dominoes of a rectilinear region is called \emph{tatami} if no four dominoes meet at any point. We describe a reduction from planar 3SAT to Domino Tatami Covering. As a consequence it is NP-complete to decide whether there is a perfect matching of a graph that meets every 4-cycle, even if the graph is restricted to be an induced subgraph of the grid-graph. The gadgets used in the reduction were discovered with the help of a SAT-solver.
Measuring the Knowledge-Based Economy of China in terms of Synergy among Technological, Organizational, and Geographic Attributes of Firms
Venue: arXiv cs.CY 2013
Year: 2013

Using the possible synergy among geographic, size, and technological distributions of firms in the Orbis database, we find the greatest reduction of uncertainty at the level of the 31 provinces of China, and an additional 18.0% at the national level. Some of the coastal provinces stand out as expected, but the metropolitan areas of Beijing and Shanghai are (with Tianjan and Chonqing) most pronounced at the next-lower administrative level of (339) prefectures, since these four metropoles are administratively defined at both levels. Focusing on high- and medium-tech manufacturing, a shift toward Beijing and Shanghai is indicated, and the synergy is on average enhanced (as expected; but not for all provinces). Unfortunately, the Orbis data is incomplete since it was collected for commercial and not for administrative or governmental purposes. However, we show a methodology that can be used by others who may have access to higher-quality statistical data for the measurement.
Reusing Precisions for Efficient Regression Verification
Venue: arXiv cs.SE 2013
Year: 2013

Continuous testing during development is a well-established technique for software-quality assurance. Continuous model checking from revision to revision is not yet established as a standard practice, because the enormous resource consumption makes its application impractical. Model checkers compute a large number of verification facts that are necessary for verifying if a given specification holds. We have identified a category of such intermediate results that are easy to store and efficient to reuse: abstraction precisions. The precision of an abstract domain specifies the level of abstraction that the analysis works on. Precisions are thus a precious result of the verification effort and it is a waste of resources to throw them away after each verification run. In particular, precisions are small and thus easy to store; they are easy to process and have a large impact on resource consumption. We experimentally show the impact of precision reuse on industrial verification problems, namely, 59 device drivers with 1119 revisions from the Linux kernel.
Graph cluster randomization: network exposure to multiple universes
Venue: arXiv cs.SI 2013
Year: 2013

A/B testing is a standard approach for evaluating the effect of online experiments; the goal is to estimate the `average treatment effect' of a new feature or condition by exposing a sample of the overall population to it. A drawback with A/B testing is that it is poorly suited for experiments involving social interference, when the treatment of individuals spills over to neighboring individuals along an underlying social network. In this work, we propose a novel methodology using graph clustering to analyze average treatment effects under social interference. To begin, we characterize graph-theoretic conditions under which individuals can be considered to be `network exposed' to an experiment. We then show how graph cluster randomization admits an efficient exact algorithm to compute the probabilities for each vertex being network exposed under several of these exposure conditions. Using these probabilities as inverse weights, a Horvitz-Thompson estimator can then provide an effect estimate that is unbiased, provided that the exposure model has been properly specified. Given an estimator that is unbiased, we focus on minimizing the variance. First, we develop simple sufficient conditions for the variance of the estimator to be asymptotically small in n, the size of the graph. However, for general randomization schemes, this variance can be lower bounded by an exponential function of the degrees of a graph. In contrast, we show that if a graph satisfies a restricted-growth condition on the growth rate of neighborhoods, then there exists a natural clustering algorithm, based on vertex neighborhoods, for which the variance of the estimator can be upper bounded by a linear function of the degrees. Thus we show that proper cluster randomization can lead to exponentially lower estimator variance when experimentally measuring average treatment effects under interference.
Dienstplanerstellung in Krankenhaeusern mittels genetischer Algorithmen
Venue: arXiv cs.NE 2013
Year: 2013

This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems. It shows that such information can significantly enhance performance, but that the choice of information and the way it is included are important factors for success.
Adaptive Alert Throttling for Intrusion Detection Systems
Venue: arXiv cs.CR 2013
Year: 2013

Each time that an intrusion detection system raises an alert it must make some attempt to communicate the information to an operator. This communication channel can easily become the target of a denial of service attack because, like all communication channels, it has a fixed capacity. If this channel can become overwhelmed with bogus data, an attacker can quickly achieve complete neutralisation of intrusion detection capability. Although these types of attack are very hard to stop completely, our aim is to present techniques that improve alert throughput and capacity to such an extent that the resources required to successfully mount the attack become prohibitive.